tag:notobiotica.posthaven.com,2013:/posts noto|biotica 2017-06-09T04:30:04Z noto|biotica tag:notobiotica.posthaven.com,2013:Post/1159860 2017-06-06T03:50:38Z 2017-06-09T04:30:04Z Why Australia's plant phrase-naming system is more interesting than it seems (Part 2)

In Part 1 of this blog (please read that first if you haven't already) I established (I hope) that the system we operate in Australia for phrase-naming vascular plants is an interesting and noteworthy initiative, and one that could perhaps be extended and explored as one part of a solution to the taxonomic impediment (the name we give to the problem that there are not enough of us and we don't have enough time to name all the organisms we need to name). 

I made a claim that the phrase-naming system has all the requirements to be regarded as a Controlled Namespace, and in fact runs parallel to, and augments, that other great controlled namespace, the International Code of Nomenclature for algae, fungi and plants

The purpose of this blog is to make two arguments, firstly that we should consider extending the phrase-naming system to all biota, and secondly (and probably more controversially) that we should explore using it to name aspects of biodiversity that are worth naming, but may not be "taxa" (whatever they are).

Extending the phrase-naming space to all biota

Botanists in Australia created their formal phrase-naming system for two reasons. Firstly, we inhabit a mega-diverse country with a partially documented biodiversity, and are all aware of "good" taxa that, despite not yet having a formal name, nonetheless are in need of recognition and protection. Secondly, and because of this, at the time we commenced work on the Australian Plant Census (APC) project, it became clear that if we included only formal names, we would mis-estimate our plant biodiversity. An intent of the APC was to harmonise taxonomy across state borders, and harmonising phrase-names is just as important as harmonising formal names. In these senses, the phrase-naming system is a simple solution to a practical problem.

The problem that we faced is not unique to botany. In many other taxonomic groups, we recognise more taxa than have yet been named. Collections with large numbers of un-named species are often partially curated using taxonomic "sorts", either physically in the collection, electronically in databases, or at least in the minds of the curators. If an important task of taxonomy (arguably the most important) is to document all known biodiversity, then these "sorts" represent documentation that's currently pretty undocumented.

A practical problem with documenting these undocumented taxa is that they are currently (except for plants) named using Locally Controlled Namespaces, or worse, Completely Uncontrolled Namespaces. If something in a collection is called "Fly sp. 1", there's not much to go on for anyone trying to understand the taxonomic concept concerned. If another collection also has a "Fly sp. 1", and if there's reason to believe that "Fly sp. 1" ≠ "Fly sp. 1", then we have a problem. This is exactly the problem that GUIDs (taxon or phrase-names) are designed to solve.

Just as with plants, capturing and rationalising these names so that we can assert (likely) equivalency between specimens having the same phrase name would be an enormous step in our task to document Australasia's biodiversity. It would give us an opportunity to capture all our knowledge, rather than just the part that's made it through all the hoops to formal naming.

Of course, this statement will immediately raise an objection in the minds of some readers. How can we be sure that these phrase-named taxa really are taxa, if we haven't yet done the taxonomic due diligence that comes with formal naming. An answer is that we work on a sliding scale, and we can't really assert anywhere along this scale that we're absolutely sure that taxon x is really a taxon. There are many cases where we can be as confident that an un-named taxon is a good taxon, as that a named taxon is a good taxon. While there will always be some uncertainty, I don't think we should let that stand in the way of a more efficient and effective way of documenting our biodiversity. 

So - I propose that, as one of the initiatives under the Decadal Plan, we extend the formal phrase-naming of Australasian taxa to all biota, and that we initiate a campaign to capture all of our current taxonomic knowledge, including knowledge that for various reasons hasn't yet made it through to formal naming. The following steps would be needed:

  1. the adoption of a single agreed convention for phrase-naming informal taxa throughout the biota (I'd like to propose the vascular plant phrase-naming convention as a bloody good start);
  2. the initiation of a campaign to capture within the agreed phrase-naming system all taxonomic knowledge represented in our collections and data systems; and
  3. commencement of a system of rationalisation between collections so that over time we can be confident that the same phrase names apply to the same taxa throughout.

Extending the phrase-naming space beyond taxa

I've described the current vascular phrase-naming system as being akin to a parking lot for taxa that await formal naming. This need not necessarily be the case, however. 

If, as I argued in Part 1 of this blog, a phrase-naming system is effectively a Fourth Namespace that sits alongside and parallel to the three existing nomenclatural Codes, it follows that we could design that namespace to do whatever we want it to do. If there are cases where we'd like to name something (i.e., do taxonomy) but we believe this is best dealt with outside the Codes, then we can design a controlled namespace from scratch and optimise it to deal with these cases.

This is where my idea of an all-biota phrase-naming system may get controversial, and I may get shot down.

Nature is immensely complex. Evolution has generated patterns of variation that are among the most challenging in the universe. Given this, is it likely that a one-size-fits-all approach to naming this pattern (one or other of the Codes depending on one's organismal group) is going to be adequate for the task?

Consider genetics and genomics. These immensely powerful tools allow us to discern patterns at a level of resolution and detail never before dreamed of. Having discerned a pattern, there's a strong desire among those of us with a taxonomic bent to want to name entities that we can discern from the pattern. If only one controlled namespace is available, that's the one we choose to name under. I think there's a danger here - that we'll bugger-up a perfectly good naming system that can't, or shouldn't, need to cope with all this extra detail.

This is one reason why I worry about "cryptic species" (I put the phrase in quotes because too often it's written without, thus rather prejudging the whole issue). Let's say that we have a lineage that's morphologically recognisable. Let's say that it was a species that currently has a name (probably dealt with using classical methods). Let's now say that genetic and genomic studies reveal well-characterised sub-lineages, which are not currently recognised in our taxonomy. Having discovered these cryptic lineages, we're tempted to name them as "cryptic species". 

This is all well and good if the point of naming is merely to document biodiversity by boffins, for boffins. The problem is that there are many more non-boffins than there are boffins, and many of these comprise "the public". I believe we ignore this at our peril. Jenny Citizen used to be able to recognise this species, but is now faced with half-a-dozen "cryptic species" that she can no longer discern. If our naming system gets loaded with taxa that she can't understand and can't see, then we'll lose her to our cause. This, of course, would be dangerous to our cause.

If there were only a small number of these awkwardly cryptic taxa, then the system would probably cope OK. If however, there are many, then loading up our taxonomy with names that are effectively useless for many (though not all) users, is a problem. My fear is that the more we look, the more cryptic variation we'll find.

And this is where the Fourth (or Fifth, or Sixth) Namespace comes in. We could design a namespace that's optimised to allow us to capture names of things (such as morphologically cryptic lineages) that we choose not to name in our Code-based namespace. Because our new namespace is a controlled one, it would still serve perfectly well for communication among the boffins and other rare breeds who need it. Our Code-based namespaces, which perhaps are more public-facing, could then be immune from being over-stuffed with these things. 

This would also have the advantage that we'd solve a current problem even for us boffins. Many researchers who discover lineages (or sub-lineages) using genetic and genomic methods, fail to name them under the Codes because they find it too hard. There's a curiously anachronistic view around that you need to find some morphological difference (any morphological difference) to be comfortable to name something under the Codes. A result is that some people work away trying desperately to squeeze some minor morphological difference out of their poor creatures, then (if they get lucky) name them on that basis. Others either give up, or don't bother. The result? Our worst enemy - an uncontrolled namespace. How many Clade A's can you think of in your group's literature? We could invent a system that works better than this.

So - I propose that we investigate a phrase-naming system that will allow us to name genetic lineages and other entities that should be named, just not under the Codes.The following steps would be needed:

  1. the adoption of an agreed convention for phrase-naming genetic lineages (and perhaps other entities such as significant populations);
  2. the establishment of standards for journal papers that will provide a convenient way for such names to be coined; and
  3. the establishment of a system to track and document these names, and that would allow them to be resolved back to an original source.

We could then inhabit the best of all possible worlds (well, that might be going too far), with several carefully controlled name-spaces each optimised for different uses. The sum of our taxonomic knowledge would be the sum of these namespaces, in whatever combination is most fit for purpose for the particular questions asked. I think this would give us much-needed flexibility, that is currently lacking in our nomenclatural system.

Over to you for comment...

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1141564 2017-06-05T07:07:27Z 2017-06-06T04:21:08Z Why Australia's plant phrase-naming system is more interesting than it seems (Part 1)

For the last decade or so, Australian botanists have been doing a very interesting thing (we've actually been doing lots of interesting things, but this blog is about just one of them). We’ve been naming taxa (or at least, putative taxa) outside the International Code of Nomenclature for algae, fungi and plants (the Code), using a parallel but carefully formulated and controlled nomenclatural system.

This is the phrase-naming system, standardised by Bill Barker on behalf of the Council of Heads of Australasian Herbaria (CHAH) in 2005 (see Barker, W.R. Standardising informal names in Australian publications, Australian Systematic Botany Society Newsletter 122, 11–12, 2005).

A phrase name is a name constructed under the agreed CHAH standard, with the form “Genus-name sp. Phrasename (Voucher specimen identifier) Source”. Some examples are Acacia sp. Ambathala (C.Sandercoe 624) Qld Herbarium, Sauropus sp. Jabiru (C.R.Dunlop 3381) NT Herbarium, and Typhonium sp. Kununurra (A.N.Start ANS 1467) WA Herbarium.

The phrase-naming system was standardised at the time the Australian Plant Census (APC) project was initiated. This is no coincidence – the APC was an initiative to checklist accepted vascular plant taxa across Australia, and a standardised phrase-naming system was required for that effort.

At first glance, our vascular plant phrase-naming system may seem prosaic and uninteresting - what's so special about putting tag names on plants? However, I reckon it's actually much more interesting than it seems. Firstly, to the best of my knowledge, it's globally unique: no other country has an agreed, formal, multi-jurisdictional standard for naming taxa outside the normal provisions of biological nomenclature. But beyond it's uniqueness, I think it establishes a precedent and a model that could provide much-needed flexibility in naming throughout modern taxonomy and systematics.

Names and namespaces

Technically, names are GUIDS (Globally Unique Identifiers). A GUID is a key (a number or text string) that identifies a thing, and that the system designer can assert uniquely identifies that thing and only that thing within the system. If this is the case, a GUID can then stand in for the thing itself. GUIDs are particularly important in globally distributed systems (like the internet, or biology), where the Globally Unique part of GUID means exactly that.

To ensure that GUIDs are globally unique, a control system and a set of rules are needed, which together control the assignment of GUIDS to things, and the resolution from GUIDS to things. If such a control system is present, and it results in global uniqueness, the system is called a Controlled Namespace. A great example of a controlled namespace is the DNS (Domain Name System), which controls how domain names (like notobiotica.posthaven.com) are assigned and managed. If the DNS didn’t control domain names as GUIDS, and two separate websites could each have the same domain name, the internet would quickly unravel.

Taxonomists around the world are very familiar with controlled namespaces, because that's what the three Codes of Nomenclature (the botanical, zoological and bacteriological Codes) are. The Codes are complex sets of rules that control how names are assigned (rules of validity), are deemed to be correct or incorrect (rules of legitimacy), and are resolved when several valid and legitimate options exist (rules of priority). The rules ensure that one taxon has one valid and legitimate name (that is, each taxon has a GUID). 

The Codes, while exceedingly important, are not perfect, largely because they evolved at a time when controlling the biological namespace was effectively impossible. Taxonomists wore funny wigs, spoke Latin, printed their taxonomy in books using Gutenberg presses, and distributed them by slow boat or a new-fangled and very cool thing called a postal service. If the internet had been invented at that time, it would be a complete mess. The fact that biological nomenclature isn’t a mess (it’s actually pretty good) is testament to the great workarounds that our nomenclatural forebears put in place at the time the Codes were consolidated in the late Nineteenth and early Twentieth Centuries.

As well as being imperfect, the Codes are not magical: they're useful only because of the controlled namespaces they enable. And if good reasons emerge to set up more controlled namespaces, there's nothing to stop us doing just that.

The fourth namespace

This is why I think the Australian phrase-naming system is interesting. It's a fourth controlled namespace. (Remember that it combines a standard rule for forming names, and a process - the APC - that ensures uniqueness, hence the phrase-name system in a formal sense is a controlled namespace.) In fact, while we often call phrase-names "informal", in contradistinction to the "formal" names created under the Codes, in many ways they're just as formal. 

This fourth namespace was created to solve a specific problem in Australian botanical taxonomy, which is that we have a bottleneck: taxa (at least, putative ones) are being recognised in Australia faster than we can deal with them under the normal mechanisms of taxonomy and name them under the Codes. The phrase-naming system was invented as a "parking bay", to enable names to be given to these taxa - with all that that implies for communication, conservation etc. - while they await "formal" naming. It's a neat partial solution to the taxonomic impediment, which of course is what causes the bottleneck in the first place. 

The thing I find interesting about this is that there are many dimensions to the taxonomic impediment, and formal phrase-names established under a controlled namespace, like the Australian vascular plant phrase-naming system, could play a larger role in dealing with these. In a later blog I'll try to draw out some of these possibilities, and to show that this fourth namespace could play a larger and more interesting role in our overall taxonomy than it does at present. It could, for example, be extended to the whole of Australasian biology, allowing the formal (informal) naming of organisms other than plants. In doing so, it could play an important role in rapidly capturing, with unique names, all our taxon concepts, even those that are not yet ready (for a variety of reasons) for naming under the Codes (or indeed, and here's a thought, ones that we have no intention of naming under the Codes).

Coming up next - extending phrase-names to the whole of life, and to more than just "taxa"...

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1160722 2017-06-05T04:22:24Z 2017-06-05T05:05:06Z Darren Crayn A long time ago, in a city far, far away... I began engineering studies.

It seemed a logical choice at the time. For a boy growing up with a sciency bent in a small and unremarkable country town in northern New South Wales, it seemed engineering as a career made sense, or so said my rather unimaginative high school careers advisor. Off to the big smoke I went, and 6 months into a chemical engineering degree, I fell in love with .... biology.

Engineering and I negotiated an amicable separation and my new crush led ultimately to a postgraduate degree at the University of New South Wales (Sydney), where I developed research skills and credibility in phylogenetic systematics of plants. After graduating I was off overseas where I worked on the evolution of photosynthesis in bromeliads, using a phylogenetic approach, at the Smithsonian Tropical Research Institute in Panama and Oxford University in the UK.

I returned home to Sydney in early 2000 and after a period of research odd-jobbing (ranging from taxonomically revising a small genus of vascular plants, to working on the genetics of gestational diabetes), I landed dream job #1: Tropical Botanist at the National Herbarium of NSW. A hugely satisfying 6 years of research and practical herbarium taxonomy ensued, until as fate would have it dream job #2 emerged, fully formed, seemingly from nowhere. Strange how the most wonderful things happen when you least expect them.

Dream job #2 is what I do now: Director of the Australian Tropical Herbarium, a joint venture between CSIRO, the Queensland Government, The Australian Government Dept. of the Environment, and James Cook University. This dynamic and growing organisation, located on JCU’s Cairns campus, aims to be a significant global player in tropical plant biodiversity research. My role is roughly equal parts management/leadership and research. The latter involves studies of the origins, evolution and classification of plants and deals broadly with the questions: how many plant species exist, where do they occur, how are they related and how have they evolved? More specifically this research is:

•       discovering, naming and classifying new plant species and determining the evolutionary relationships among them,

•       mapping the distribution of ecosystems, species and genetic variation within species across the landscape,

•       developing DNA-based tools and ‘matrix keys’ for species identification and rapid biodiversity inventory

•       uncovering the deep-time origins and ancient migration pathways of plants that are found in tropical Australia today

I’ve been lucky enough that research has taken me to many biomes and countries including the Republic of Panama, Venezuela, Papua New Guinea, Indonesia, New Caledonia, Malaysia, New Zealand and the United Kingdom.

In addition to institutional and science community leadership and research roles, I contribute to biodiversity and science policy development and implementation through roles on a number of advisory committees and expert panels for the Australian and State governments, and the non-governmental research sector.

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Darren Crayn
tag:notobiotica.posthaven.com,2013:Post/1160718 2017-06-05T03:31:58Z 2017-06-08T23:29:56Z David Yeates

I am an insect systematist and Director of the Australian National Insect Collection.  I hold an adjunct Professorship at the Australian National University and am also the Schlinger Curator of Diptera at ANIC.  After a stint as Roosevelt Postdoctoral Fellow at the American Museum of Natural History in New York, I returned to Australia teaching systematic entomology at the University of Queensland.  Not long after the Department of Entomology was amalgamated into a larger department at UQ I moved to Canberra to begin work as a research scientist at the Australian National Insect Collection.  I became the Director of ANIC in 2012.

My main interests are in the systematics and taxonomy of insects in general, and flies (Diptera) in particular, with special interest in Australian flies.  I have always had a strong interest in teaching and outreach, and promoting the importance of the work that taxonomists do.  Way back in my career I worked with Kevin Thiele to develop the Lucid system of interactive keys.  My current work includes molecular phylogenetics of insects, flies and various families of flies including the Bombyliidae (bee flies), Therevidae (stiletto flies), Stratiomyidae (soldier flies), Fergusoninidae, Tachinidae (bristle flies) and Tabanidae (horse flies), all done in collaboration with PhD students and postdocs.  I also teach undergraduate entomology at the Australian National University. 

Australia is an amazing place to be an invertebrate systematist.  With most of the fauna undocumented there are major discoveries to be made just outside every laboratory.  Because of the deep time history of Australia, and its preservation of habitats that have disappeared elsewhere on earth, very old lineages still find a home here.  In addition, due to the dramatic climatic changes in Australia through the last 60 million years, many groups have responded by radiating rapidly into new habitats. This combination of arks and cradles of diversification create compelling foci for taxonomic, systematic and evolutionary studies.

My research career has seen the advent of single gene molecular systematics, then through the dark days of multilocus molecular systematics using Sanger sequencing, and am now very pleased to have emerged into the light of high throughput sequencing (HTS).  Now various approaches can be used to assemble datasets that contain a very large portion of the genome through transcriptome sequencing and genome reduction techniques such as hybrid enrichment.  I am very excited about the promise of HTS for extracting large chunks of the genome from museum specimens, adding another important dimension to the value of biological collections.

Systematic entomology has an important role to platy in biosecurity within the broad scope of food security.  Because of its isolation, and strong biosecurity processes, Australia is free of many of the world's most devastating pests and diseases.  This has multiple benefits for our industries in terms of lower production costs, and access to premium markets overseas. In order for these benefits to continue, Australia needs to build and maintain capability in diagnosing the groups that pose a biosecurity threat.  We also need to be able to quickly distinguish the threats from the native fauna.  In many cases this is not trivial - Australia is home to large numbers of species that are very often challenging to distinguish from invasives.  This brings an important economic dimension to entomological systematics.

I have written a couple of pieces for the Conversation relevant to this blog site:

Why so many Australian species are yet to be named?

Australia: riding on the insects back

Hidden housemates: we live with a zoo of harmless mini-beasts

Insects are the great survivors in evolution



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tag:notobiotica.posthaven.com,2013:Post/1154592 2017-05-17T03:13:52Z 2017-05-17T03:28:53Z The Decadal Plan is mission go

An email on Monday from Prof. Andrew Holmes, President of the Australian Academy of Science, and an Academy news release, formally announced the commencement of an intensive project to develop a Decadal Plan for Biosystematics and Taxonomy in Australasia. The support provided for this initiative from the Academy of Science, the Ian Potter Foundation, and the project’s partners, is very welcome, and we’re very excited that work is commencing in earnest..

The plan is to release an Exposure Draft of the Decadal Plan in late November, at the joint meeting of the Australasian Systematic Botany Society and the Society of Australian Systematic Biologists in Adelaide, with the final Plan to be released in early 2018. In the lead-up to release of the exposure draft, there will be much work for the project’s Working Group and Steering Committee. We hope that many practicing biosystematists and taxonomists, and stakeholders, will be able to contribute and to engage in development of the Plan. It’s success is obviously contingent on meaningful engagement with as wide a range of contributors as possible. This project gives us all the opportunity to contribute to strategic development of the twin disciplines of biosystematics and taxonomy in our region, and to shape their future, impacts and achievements.

During development of the Plan, discussion papers and pre-release drafts of sections for comment and discussion will be released in noto|biotica, and through our sector’s social media. We welcome any comments, views, feedback and contributions, either directly through this site or by email to me or to other members of the Working Group (I’ll shortly update a contact list for Working Group members here). We plan also to arrange a series of sector and stakeholder meetings in capital cities throughout Australia and in New Zealand. Please also share news of our plans with your colleagues and through your own social media channels, and encourage others to get involved.

The overall goal of the Plan is to map out where we want biosystematics and taxonomy in Australasia to be in 2028, what achievements we would like to see realised, and what’s needed to get there. We encourage you all, whether practicing biosystematists or taxonomists, or stakeholders, to put your thinking caps on, decide what you think the priorities should be, discuss with colleagues, and share your thoughts with us.

 We look forward to working with you all.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1144951 2017-04-08T09:14:36Z 2017-04-08T09:51:18Z Francis Nge

I'm a PhD candidate currently based at the University of Adelaide & State herbarium of South Australia.

I've just completed my Honours at the University of Western Australia (UWA), under the supervision of Kevin Thiele & Michelle Waycott, where we discovered four new species of Banksia (and two potentially new species pending further investigation)! 

I'm still at the planning stages of my PhD, however, I'm certain that taxonomy and systematics will be a core component of my project. My project will focus on the biogeographic and phylogeographic relationships of the South Australian temperate flora, in relation to the wider temperate Australian region as a whole. Many studies have focused on either the southwest or southeastern regions of Australia, with the Adelaide-Kangaroo Island region in South Australia being overlooked even though it is identified as an endemism center – one that contains many species and genera with disjunct distributions across the Nullarbor and Murray-Darling basin. Understanding the historical processes that have resulted in these distributions will require the integration of multiple fields, with practical implications for taxonomy, systematics, conservation biology, and in advancing our understanding of evolutionary processes that have occurred across the region as a whole.

I'm also currently involved in a number of other projects, including one with Hans Lambers where we looked at the host preferences of quandong (Santalum acuminatum) in both an ecological and physiological context. I'm also involved with the Kwongan Foundation (http://www.facebook.com/kwonganfoundation/) where we aim to achieve UNESCO World Heritage listing for the biodiverse region of southwest Western Australia. I also try and engage with the wider community in promoting taxonomic knowledge and its importance by showcasing the diversity of life through social media channels (e.g. http://www.instagram.com/francisnge/).  

I've always been fascinated about the natural world, but it wasn't until a couple of years ago while completing my undergraduate degree in botany at UWA that I'd realised taxonomy underpins all other fields of biology, and is crucial in advancing our understanding of the immense diversity on earth. Despite the crucial role that we play, our work are often under appreciated (from both the scientific community and the general public), hence I fully support the Decadal Plan. 

I am keen to learn from all the great minds and experienced researchers/ botanists here, and hope to meet you in the near future. :)

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Francis Nge
tag:notobiotica.posthaven.com,2013:Post/1142735 2017-03-30T23:07:44Z 2017-04-05T23:34:48Z Sue Fyfe

I’m the Director of the Biodiversity Science Section at Parks Australia, Commonwealth Department of the Environment and Energy (DoEE). This section incorporates the Australian Biological Resources Study and associated Bush Blitz species discovery program, the National Seed Bank, Parks Science and Knowledge Management team, Biodiversity Informatics team, and Parks Australia’s long term partnership with CSIRO in the Centre for Australian National Biodiversity Research including the Australian National Herbarium. 

I’m not a taxonomist but I have had a long and varied career in plants and marine and terrestrial ecology, which led me into the public service some 12 years ago. I began my working life as a horticulturist, and after further landscape qualifications and 2 years as the Landscape Architect’s assistant at Kiama council, I established and ran a landscape architecture partnership specializing in the restoration of native vegetation in industrial and suburban developments for about 10 years in the Illawarra region. A desire to know more about the science behind environmental rehabilitation led me (part time) into a BSc (Honours) focused on vegetation biogeography, ecology and spatial science at the University of Wollongong, and environmental consultancy work. I completed a PhD on seagrasses at UoW in 2004 combining plant physiology and ecology with hyperspectral remote sensing while continuing with consulting work, lecturing and research contracts to pay the bills.

I joined the Australian Government (then) Department of the Environment and Heritage in December 2004 and have been in Canberra ever since. I have broad experience in executive level government roles, including applying scientific and spatial data to environmental management, policy and program development, marine bioregional planning, and strategic information, including 6 years leading Geoscience Australia’s science data stewardship, information management and eResearch initiatives. I have a passion for both terrestrial and marine biodiversity and ecology, and for online, open access to science data and information.

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tag:notobiotica.posthaven.com,2013:Post/1142630 2017-03-30T16:40:44Z 2017-03-30T16:40:44Z Matt Barrett

I’m a Research Scientist with Kings Park and Botanic Garden in Western Australia, also an Adjunct at the University of Western Australia and Research Associate at the Western Australian Herbarium.

I started out with a passion for reptiles, lacewings, fungi and plants of the Kimberley region where I grew up, and eventually meandered (via chemistry and engineering degrees) into a PhD on population genetics of wax flowers (Chamelaucium) in south-west WA. Since then I have worked on population genetics and reproductive ecology of rare plants (Lepidosperma and Darwinia), and phylogenetic systematics of major Australian plant lineages - Chamelaucium-Darwinia-Verticordia group (Myrtaceae), Lepidosperma (Cyperaceae), Aphelia, Centrolepis and Gaimardia (Centrolepidaceae/Restionaceae), Lazarum and Typhonium (Araceae), Eriachne and Micraira (Poaceae subfamily Micrairoideae), tropical Boronia (Rutaceae), Solanum (Solanaceae), and many genera of tropical fungi. In my 'spare time’ I do the most important job of all, describing new species of plants and fungi (> 60 spp. so far with many more to come). Many of these new species have come from extensive surveys of sandstone pavements in the Kimberley, an overlooked complex of communities containing numerous short-range endemic taxa.

Most recently I have run an extensive ARC-funded project on Triodia hummock grasses (‘spinifex'), one of the dominant arid and semi-arid plant groups of the Australian outback. The Triodia project has investigated the phylogenomic relationships and biogeography of both the genus and several species complexes, and resulted in the discovery of numerous new species - papers in progress will almost double the number of species in the genus (to at least 120 species), making Triodia the largest grass genus in Australia. I have also intensively surveyed polyploidy in Triodia, uncovering the existence of many geographically-separated polyploid ‘races’ in the Pilbara, with substantial implications for the seed collection industry. Benjamin Anderson, a recently-completed PhD student associated with this project, has produced an excellent series of papers on the Triodia basedowii complex, ultimately recognising 8 new species and providing significant insights into diversification in this characteristic arid-zone species-complex (taxonomic paper just accepted in Aust. Syst. Bot.). A Lucid key for identification of Pilbara Triodia is in development, and will hopefully eventually be expanded to cover the whole genus.

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Matthew Barrett
tag:notobiotica.posthaven.com,2013:Post/1141405 2017-03-25T05:52:03Z 2017-04-05T00:41:02Z Flowers in uv and false bee vision.

Wild radish (Raphanus raphanistrum) flower in natural colour (left), uv only (centre) and false bee colours (right).

We’re attracted to flowers because of their form, scent, and colour, the very things that attract their pollinators. It’s clear that some colours are associated with particular pollinator groups, like red for birds and blue for bees. However, most pollinating animals perceive a different colour spectrum from us. Humans are unusual—but not unique—among mammals in having three colour receptor genes, which code for opsin proteins whose light reception peaks in the blue, green, and red wavelengths. Some people—more often males than females because of sex-linkage—can perceive only two, usually blue and green. For them red and green may be indistinguishable, or red appears as black, and hues like purple that mix red with another colour will not look the same as they do to people with three-colour vision. There are websites that show what the world looks like to people with fewer than three opsins. This is important, because none of us can see one of the colours that birds and bees can see, ultraviolet; so we’re a bit like colour-blind bees, if such things exist (I wouldn’t be at all surprised to find they do).

It seems that early mammals were nocturnal and sacrificed full colour vision for eyes that had many more rods, enabling better, but monochromatic, night vision. Through opsin gene duplications and divergence of the colour sensitivity of the duplicated genes, many mammals have regained second opsins and a few, like humans, even regained a third. This is engagingly described by Richard Dawkins in “The Ancestor’s Tale”. But non-mammal vertebrates like birds, lizards, and fish can have more opsins, often three similar to the three human ones plus one that perceives a portion of the ultraviolet part of the spectrum. Many insects on the other hand, have three opsins that perceive uv, blue, and red.

All this indicates that if we’re to understand colour as an attractant for pollinators, we need some way to study the ranges of flower colours that the pollinators can perceive. Often this means using a spectrometer to measure the reflected wavelengths as by Bischoff et al. (2013). But an important aspect of flower colour is the arrangement of contrasting patterns in flowers, like stripes and spots that function as nectar guides and ensure insects are both attracted and aligned correctly in the flower to find the rewards and accomplish pollen transfer. One way to study these patterns is through photography.

Viola banksii flower in natural colour (left), uv only (centre) and false bee colours (right).

First, I’ll describe how to photograph just the uv portion of the reflected light from a flower. Then I’ll describe how to simulate the flower’s reflectance across the whole spectrum perceived by an insect.

Photography in uv light.

Digital photography has made uv photography easy in some ways and hard in others. It’s hard, or at least expensive, because most modern digital cameras have very effective filters that prevent the sensor from recording any uv or infra-red light. There are some very expensive uv-sensitive cameras that are used in forensic work (bruises can be detected in uv light long after they’ve faded from normal vision). But we’re in luck because a few older DSLR cameras are weakly sensitive to uv light, and these are still available second hand. One of the reliable ones that many people use is the Nikon D70. I bought a couple of good ones on line for about $200 each, although one has an occasionally sticky shutter.

Secondly, many lenses have numerous glass elements and glass absorbs uv light. There’s another problem too: most lenses focus uv light slightly differently to the optical wavelengths, and because we can’t see the uv we have no way of focusing the image before we take the picture. You could pay $10,000 for a quartz lens to eliminate these problems, but there are adequate cheaper solutions. The EL-Nikkor enlarger lenses often transmit enough uv light because as fixed-focus lenses they need fewer glass elements. The different models vary in their uv transmission and their ability to focus close to the visible range. Overall the EL-Nikkor 80mm f5.6 seems to be the best bet. As a bonus, it’s a pretty good close-up lens with a couple of sets of rings or a bellows. I got a couple of used ones on line for about £40 each, and I see them popping up for sale every few weeks. Note there are two versions of this lens and the one that’s recommended is the older type that has some chrome (not all black) on its outer parts. I found this blog post, which compares some of these Nikkor enlarger lenses and the site has many other very useful posts and great images. 

Various sites recommend a focussing helicoid to make up for the EL-Nikkor being a fixed focus lens. I bought one, but I don’t need it for close-up shots, because I’m using close-up rings and so I can simply focus by moving the camera with the tripod. But if you want to photograph landscapes in uv or infra-red (IR) with this lens, you’ll need a helicoid. Either way, you will need a connecting ring to join the lens’s screw mount to the helicoids’s or close-up ring’s bayonet mount (eBay).

Next, you need to block all visible light, because the sensor is orders of magnitude more sensitive to it than to uv light. There are several uv pass filters available that block all visible light while allowing uv through. But most of them, and unfortunately those that are reasonably priced, also let IR through, and the camera sensor is also much more sensitive to IR than to uv. So if you use those, your photo will be an IR, rather than uv, image. What you need is a so-called Venus filter, made by Baader, and designed for astronomers to photograph uv reflectance from Venus. I got mine new from Baader’s Australian agent. It’s probably the most expensive item in the kit.

Important safety warning: never use this filter to look at the sun or to photograph the sun. Although it blocks all visible light, remember that invisible, but very dangerous, uv light is pouring through it.

There’s an additional problem: attaching the filter to the front of the lens. The filter holder on the EL-Nikkor lens has an unusual diameter (34.5 mm, while the filter is 52 mm), but there’s an engineer in Belarus who makes 34.5–52 mm connecting rings, available through eBay. Or you could get a 34–52 mm connection and glue it onto the lens.

Finally you need a light source that produces uv, and again this is a problem because standard flashes are filtered to protect our eyes from damaging uv wavelengths. Following recommendations, I bought a Vivitar 285HV flash, and asked a technician to remove the filter (there’s a YouTube instructable for how to do it, but I didn’t want to do it myself for fear of electric shock from the capacitor). Alternatively, you can use sunlight, but that’s better done outside (because window glass filters out some uv) so you run into trouble with wind movement in long exposures. It doesn’t matter that the flash also produces a lot of visible light, because the Venus filter blocks it all. I’m not sure, but I hope using the uv-enabled flash is not too damaging to the eyes, so long as you don’t ever fire it towards a face.

Nikon D70 camera, two sets of close-up rings, EL-Nikkor 80 mm f 5.6 lens, and Baader Venus filter (left) and modified Vivitar flash (right).

So that’s the kit. It took me a couple of months to pull it all together and it probably cost close to $1000. There are other options, but this was based on what seemed like the most knowledgeable advice I could find on line.

How do I use it? First, I use visible light to arrange my subject and focus the camera, set to manual. Then I screw on the filter, set the camera to take a 10 second exposure and while the shutter is open I fire the flash a couple of times at very close range, from the left and right sides of the flower. You can use a cheap infra-red remote to avoid camera shake, but if you give it a second to settle before firing the flash that won’t be a problem. I hold the flash in my hand and fire it manually while the shutter is open. It’s important to try to avoid shadows, because these can look falsely like uv absorbing regions, especially when you come to assemble false colour images. A uv-enabled ring flash would be ideal I think.

You can ramp up the ISO setting, and I tend to use an f11 aperture although f8 would help brighten the image. Even with the flash so close, the image is often pretty pale, so sometimes f8 is necessary.

Sometimes there are uv-absorbing regions in flowers that you wouldn’t expect from the visible range, and that’s what is fascinating about this. In musk, for example, the lower corolla lobe is uv dark, while the others reflect. In Genista stenopetala, the keel and wings absorb uv while the standard reflects it, although its corolla is uniformly yellow to our eyes.

Simulating insect vision.

Unfortunately, people sometimes jump from “insects can see uv” to thinking uv photos show what insects see. They don’t. Bees and many other insects see complex colours made up of uv, blue and green, in the same way we see colours made up of blue, green, and red. 

Each pixel on a TV or monitor is a colour based on the contribution of blue, green, and red to that point. If insects had TVs, they’d display colours based on contributions of uv, blue, and green to each dot, but we’d only be able to see the blue and green components. We have no idea what uv looks like or how it mixes with blue and green. All we can hope to do is to replace our blue, green, and red channels with uv, blue, and green channels. Now the uv signal looks blue to us, the blue green, and the green red. This process shifts the bee-visible spectrum into the range of wavelengths that are human visible, in much the same way as a musician might transpose a song from a low into a high key: the relationship between the notes and the chords is the same, but it sounds different in a higher key (we can do this with low frequency whale calls by transposing them into a higher frequency that we can hear).

How do we do this in practice? You need two identical exposures, so it needs a firm tripod. First photograph the flower in visible light, and then repeat the exposure in uv only, by using the filter and uv flash. It takes a bit of trial and error to make sure the two photos are similarly exposed, but you can adjust a lot with Photoshop or GIMP. I tend to open the aperture a stop between taking the colour image and the uv image and of course the uv photo is taken with the much brighter light of the flash at close range.

I’ll now describe what I do in GIMP to bring these two images together as a false colour representation of what a bee might see (false colour because it’s in the human colour palette, even though it shows the colour contrasts that a bee would see).

I start with the uv photo. As it comes off the camera it’s usually in pink or purple hues (the red and blue sensors respond best to the uv light. Here are the raw colour (left) and uv-only pictures of a musk flower (Erythranthe moschata) combined side by side in one picture but not otherwise modified.

Open the uv image first. I usually convert the uv picture to monochrome by dragging the saturation slider all the way to the left. 

Then usually I need to adjust the brightness. Most times the automatic setting does this pretty well.

That’s your basic uv picture, but it’ll need to be aligned exactly to the colour one, so I crop it to a convenient size and shape (usually square) and centre it on a distinctive pixel somewhere. There are a couple of ways I’ve figured out to do this, but it doesn’t matter how you do it so long as the uv and visible colour pictures are cropped to exactly the same dimensions and the crops are centred on the same pixel (in practice it can be a tiny bit out without too much damage). Once you’ve cropped it, save it, in tiff if you’re fussy, or jpg is probably fine.

Next open the colour photo. Set the brightness either manually or auto, and then crop it exactly the same as the uv one. 

Then in the colour menu decompose it into its three colour channels: red, green, and blue. 

On screen you’ll see a new image in monochrome, which will actually be made up of three layers, one for each colour channel. Now add the uv photo as a new layer, to give you four layers: uv, blue, green, and red.

Go back to the colour menu and compose the picture again, setting the blue channel to use the uv layer, the green channel to use the blue layer, and the red channel to use the green layer. The red layer is not used. Watch your new false colour image appear on screen!

These false colour pictures still need a little care in their interpretation. The pink and orange musk flower is unlikely to be what a bee sees, but any contrasting colour patterns we can see (not always seen in the human-colour palette) will be visible to a bee. We have no idea what a bee experiences when it sees a flower in its uv-blue-green colour palette, any more than we know what infra-red or radio waves might look like.

And of course the choice of which channels to fill with which colours is entirely arbitrary. Here's the musk flower again, this time with blue in the blue channel, green in the green channel, and uv in the red channel.

Birds can see uv as well as blue, green, and red. Not only do we not know what uv looks like, but we can’t begin to guess what its colour combinations look like, such as uv+blue+red. It’s like visualising four dimensions in only three, with the added problem that we can’t conceive what one of the dimensions looks like at all. Most New Zealand flowers visited by birds tend to reflect strongly in uv and red and absorb blue and green wavelengths, appearing just red to us but some unknowable blended colour to their pollinators.

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Phil Garnock-Jones
tag:notobiotica.posthaven.com,2013:Post/1140900 2017-03-23T01:14:38Z 2017-03-24T19:32:27Z Phil Garnock-Jones

I’m a retired plant taxonomist in Wellington New Zealand. Before I retired, I entertained the idea of giving up botany and taking on something new, but it hasn’t happened. So much taxonomic research these days requires a lab and students, to say nothing of keeping up with a ballooning literature. But there’s still a lot that can be done from home: Flora contributions, field guides, illustration, photography, and simple garden experiments. I have two major projects on the go right now. 

First, I’m tying up the last loose ends of a draft Flora of New Zealand treatment of Veronica (141 NZ species). Veronica is our largest genus—although Carex is racing towards taking over that distinction—and we have 122 native and 19 naturalised species. The new Flora treatment draws on previous monographic work on the native species (Bayly & Kellow 2006, Meudt 2008, Garnock-Jones & Lloyd 2004, Garnock-Jones 1993). The task was to compile new comparable descriptions for these and the naturalised species. I have been able to use Bill Malcolm’s photos from Bayly & Kellow (2006), which cover 90 species, and I’ve been able to take new photos, covering the same character set, for the additional 50 (like Veronica spectabilis, below). The Flora treatment will appear in the on-line Flora of New Zealand and as a PDF download.

This photography led me into my second major project, which is more open-ended: flower and fruit photography. It started with fulfilment of a long-standing dream, to take photos of New Zealand flowers’ ultraviolet reflectance, hard to do with the old film cameras. I needed a digital SLR camera, lens, uv pass filter, and uv light source. The DSLR was such a step above the excellent point-and-shoot I had been using and it’s led me into a whole new world. As a result, I have a growing collection (maybe 500 species) of flower close-ups, mostly of New Zealand native and naturalised plants. I’m happy to make these available (free to colleagues for research publications and most conservation projects); just ask.

Nothing comes from nothing, and so I’ll finish with an outline of where I’ve come from. My PhD was on taxonomy of Parahebe (now part of Veronica). My first job (1975–1994) was in Christchurch at Botany Division of the Department of Scientific & Industrial Research (CHR), where I spent 1975–88 working on Brassicaceae, Caryophyllaceae, Asteraceae and others for our naturalised dicot Flora (Webb, Sykes, & Garnock-Jones 1988) and developing an interest in explicitly evidence-based systematics (hence cladistics and molecular phylogenetics). In 1994 I moved to Victoria University of Wellington, where I taught botany, evolution, and systematics until 2012. Through collaborations with Te Papa botanists and a sequence of excellent students I was involved in a range of projects on Veronica, Scleranthus, Plantago, Gesneriaceae, and Wahlenbergia. Along the way, I’ve also been involved with molecular identification of components of herbal remedies and the evolution of sexuality in land plants. I still have a desk at VUW, where I’m an Emeritus Professor and even do the odd spot of teaching.

I’ve been blogging elsewhere, but haven’t added anything there in quite a while. 


Bayly M.J.; Kellow A.V.  2006. An illustrated guide to New Zealand hebes. Wellington: Te Papa Press.

Garnock‑Jones, P.J.  1993. Heliohebe (Scrophulariaceae ‑ Veroniceae), a new genus segregated from Hebe. New Zealand Journal of Botany 31: 323–339.

Garnock-Jones, P. J.;  Lloyd, D. G. 2004.  A taxonomic revision of Parahebe (Plantaginaceae) in New Zealand.  New Zealand Journal of Botany 42:  181 – 232.

Meudt, H.M. 2008. Taxonomic revision of Australasian snow hebes (Veronica, Plantaginaceae). Australian Systematic Botany 21: 387–421. 

Webb, C.J.;. Sykes, W.R; Garnock‑Jones, P.J.  1988. Flora of New Zealand Vol. 4 Pteridophytes, Gymnosperms, Dicotyledons. Christchurch: Botany Division, DSIR.


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Phil Garnock-Jones
tag:notobiotica.posthaven.com,2013:Post/1140898 2017-03-23T01:03:28Z 2017-03-23T01:06:13Z Alexander N. Schmidt-Lebuhn

After completing a PhD in Göttingen, Germany, and postdocs in Germany and Switzerland I started as a CSIRO research scientist at the Australian National Herbarium in Canberra in 2010. My primary study group are the Asteraceae, and from a systematics perspective in particular the native Gnaphalieae (everlasting paper daisy tribe). My research interests, however, are broad and have always been, including molecular phylogenetics, species delimitation, user-friendly identification keys, pollination, polyploidy, spatial patterns of biodiversity, and, increasingly, conservation genetics.

Currently I am building a Lucid key to the Cassinia group, am involved in a project on estimation of viable plant population sizes, and continue working towards a well-resolved phylogeny of Australian Gnaphalieae using high-throughput sequencing. I am also an ANU Academic Visitor and have contributed to undergraduate teaching. I enjoy reading, playing board games and photographing plants.

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tag:notobiotica.posthaven.com,2013:Post/1138407 2017-03-14T01:29:06Z 2017-03-14T02:02:21Z Lizzy Joyce

I’m a PhD candidate at James Cook University in Cairns with the Australian Tropical Herbarium. While completing my honours project working on the taxonomic resolution of the Tetratheca hirsuta complex at the Western Australian Herbarium I was hooked by the juicy questions that systematics can answer, the fundamental importance of taxonomy and how much there still is to be understood about the Australian flora.

I am currently in the early stages of my project which focusses on the origins of the northern Australian flora and specifically the role of exchange between Sunda and Sahul. By comparing published and unpublished dated molecular phylogenies for the region and generating new phylogenies I’m trying to get a picture of the temporal patterns in divergence events that contributed to making the northern Australian flora the way it is now. I’m also interested in trying to identify some of the main factors driving divergence in this region on a broad scale.

Aside from trying to get to the bottom of these questions, the opportunity that this project gives me to work with researchers from a number of disciplines and work with multiple groups of plants is really exciting for a plant nerd like me. What better way to spend the next few years! (OK, I might be in the honeymoon period of my project but just let me have it…)

I’m passionate about the importance of systematics and taxonomy and, as a new kid on the block, view the Decadal Plan as a necessary and encouraging step towards promoting this field and securing its future.

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tag:notobiotica.posthaven.com,2013:Post/1137167 2017-03-09T07:37:36Z 2017-03-09T07:37:38Z Katharina Schulte

 

I am a molecular systematist and evolutionary biologist with a research focus on tropical plant biodiversity. My research interests lie in understanding the diversification of species-rich tropical plant groups in time and space, and the underlying factors that shaped today’s diversity. I am using molecular tools such as high throughput DNA sequencing to reconstruct evolutionary relationships and historical biogeography, investigate differences in speciation and extinction rates between lineages and examine correlations with other factors, such as past climatic change, the development of putative key innovations or other significant morphological/physiological traits.

Since 2010 I am working at the Australian Tropical Herbarium where I have the pleasure of leading the orchid research program. My current research projects employ genomic approaches to reconstruct phylogenetic relationships and the spatio-temporal evolution of Australia’s major orchid lineages, in particular the highly diverse orchid tribe Diurideae (the Donkey, Spider, Leek orchids and Co.), the subtribe Pterostylidinae (the Greenhood orchid alliance), and the two epiphytic plant mega genera Dendrobium and Bulbophyllum. A greater understanding of these orchid groups is key for the establishment of a more stable and widely accepted taxonomic classification for Australasian orchids.

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tag:notobiotica.posthaven.com,2013:Post/1137137 2017-03-09T05:12:50Z 2017-03-09T05:18:54Z Michelle Waycott

As a botanist (#iamabotanist) I have so many areas that interest me and which I work on. I believe that we should share our knowledge and expertise as a member of the community, and seek to do that in my Professional roles. 

I currently have a position as the Professor of Plant Systematics at the University of Adelaide, School of Biological Sciences and am also the Chief Botanist for the State Herbarium of South Australia. The Herbarium and the South Australian Seed Conservation Centre, are the science team within the Botanic Gardens and State Herbarium within the Department of Environment, Water and Natural Resources. My research team investigate questions of taxonomic, systematic, evolutionary and population genetic processes, often working at the interface of these disciplines. I have a particular (some say peculiar) interest in seeing even the most fundamental of our science applied in decision making. I also have a love for many groups of plants, for example I have worked for more than 20 years on seagrasses, the peculiar submerged marine plants that are found around the world in shallow waters and which play an important role in coastal ecosystems. I have studied their evolution, ecology, management and general biology but also am reviewing their taxonomy and evolutionary systematics which these days we do with amazing genomic molecular genetic tools that allow us to get DNA sequences and compare regions of the genome from hundreds and thousands of loci to inform our questions, its an exciting time to be a molecular geneticist.
 Collecting seagrass in San Blas Panama (some time ago... ;)

My group today continues to work on seagrasses but we also have research into many groups such as those I share with John Conran–Drosera and carnivorous plant evolution, many groups of monocots, tracking down just what the fossils are in new and old deposits and improving our understanding of the South Australian flora.

Since becoming the Head of the Herbarium in South Australia in 2011 I have seen great fluctuations in the interest and support that managers, decision makers and the community at large have in the work some in the field of biological systematics. Given it is such an exciting area–discovering new species, supporting decisions about conserving and managing the native species diversity of Australia, uncovering amazing features of our plants and animals and sharing these with the community and even revealing historical facts about our collections or our flora–we do not do a great job of getting other people excited by the fruits of our labour.

I view a commitment to improving the way we value biological systematics in the Science and Policy sectors as crucial to our future. 


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tag:notobiotica.posthaven.com,2013:Post/1137130 2017-03-09T03:57:45Z 2017-03-09T03:57:45Z Anthony Whalen

I'm the General Manager of the Australian Biological Resources Study; based in Canberra. I have a broad interest in Australian taxonomy, systematics, bioinformatics and conservation biology. I am strongly motivated by work that helps raise the awareness, understanding and appreciation of the Australian plants, animals and natural systems. Previous to this I worked in the a number of positions in the Australian Government's Department of the Environment (and its many taxonomic and nomenclatural synonyms). These roles included Species Information, Natural Heritage, Heritage Policy, the National Landcare Programme and Wildlife Trade.

My team and I are currently working on the Flora of Australia as one of our key priorities. With the help of the Atlas of Living Australia, Kevin Thiele and others, the Flora is rapidly evolving via a new dynamic e-flora platform. I am hopeful that resources such as the Flora of Australia can be highlighted within a Decadal Plan for Taxonomy and Biosystematics - in part for the role they can play to inform research and policy - but also to underline the importance of appropriately resourcing and developing such tools into the future.

I look forward to seeing the Decadal Plan go forward.

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tag:notobiotica.posthaven.com,2013:Post/1137126 2017-03-09T03:13:48Z 2017-03-09T04:02:26Z The Botany Bill

The American Society of Plant Taxonomists (ASPT) has been instrumental in negotiations towards a Botany Bill (formally, The Botanical Sciences and Native Plant Materials Research, Restoration and Promotion Act) recently introduced to the US House of Representatives by a Democrat-Republican co-sponsor pair. The aim of the Bill is to "support the botanical science capacity of the federal government". A press release on the Bill is here.

An interesting idea (and of course, an interesting time to introduce such a Bill in the US. To my knowledge, Trump has yet to tweet his opinion on the Bill.)

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1137121 2017-03-09T02:56:43Z 2017-03-17T11:51:08Z Ryonen Butcher

Hello – I’m Ryonen Butcher, and I’m a member of the world’s oldest profession – taxonomy. [Hi Ryonen!] My descent into this publicly-shunned and socially-misunderstood world began when I embarked on a BSc Honours project to resolve the Sphaerolobium macranthum Meisn. complex in south-western Australia. Little did I know that this was just a gateway project and that soon I’d need more… First I re-circumscribed one species and reinstated two others, but it wasn’t enough. Soon after, I recognised my first new species in the genus, and I was hooked. Before I knew it, there were publications… Oh. My. God - the high! THE HIGH!! Species followed species and genus followed genus as I spiralled into the all-encompassing vortex of plant taxonomy in a biodiversity hotspot. I’ve dragged others into this life, infecting the susceptible and excitable minds of university students with my obsessions and passions... It’s been years since I’ve seen my mother. I send her reprints to let her know I’m okay, but still she cries over the phone – Why? Why couldn’t you be a lawyer?? I’m sorry mum. I’m sorry…

(Ryonen counts SphaerolobiumMirbelia and Tephrosia (Fabaceae), Synaphea (Proteaceae), and Tetratheca and Platytheca (Elaeocarpaceae) among her addictions. She needs help. For obvious reasons.)

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tag:notobiotica.posthaven.com,2013:Post/1131147 2017-02-14T07:38:26Z 2017-03-09T03:01:01Z What are the big questions in plant systematics? - a report of a symposium on the future of global plant systematics

An interesting article in the last issue of American Journal of Botany. See especially the section discussing the big questions in plant systematics, and how we can address them. Thanks to David Cantrill for bringing this paper to our attention.

From the introduction to the paper:

"Forty botanists from 13 countries met this March in Amsterdam at a special colloquium at the Royal Netherlands Academy of Arts and Sciences to discuss the future of plant systematics (“Beyond the Tree of Life: the Future of Plant Systematics”; Fig. 1). The meeting was funded by the Netherlands Royal Academy and organized by Erik Smets (Naturalis Biodiversity Center, Leiden, Netherlands) and colleagues*; it addressed several paradoxes in our field. First, with an ongoing planetary-scale biodiversity crisis, the need for plant systematists has never been greater, and yet taxonomic expertise appears to be in steady decline, as noted by repeated calls for action (e.g., de Carvalho et al., 2007Drew, 2011). Despite this, new plant species are continuously being discovered, and plant systematics as a field has survived and even thrived, thanks to the common overarching goal of building and understanding the Tree of Life, spurred by the availability of new technology and powerful analytical frameworks. Yet, members of the public and colleagues outside biology often express surprise when new plant species are discovered or appear unaware that the Tree of Life is far from being fully resolved. In this context, how do we justify the importance of continued research on plant biodiversity and explain its importance to the general public, university administrators, funding agencies, and policy makers?"

Among other things, the colloquium asked the question "What are the cool, achievable questions in plants sytsematics, and how can we answer them?". Here's their answer:

"The third discussion session aimed at formulating questions and solutions that plant systematists as a community may realistically target in the near future. Four tentative key questions emerged: (1) How is plant life related, and how is diversity distributed in time and space? (2) What are the processes generating biodiversity? (3) How many species are there, and what do we know about them? (4) How do we break the barriers for training and employing systematists in the developing world? To address these questions, we thought that a flagship international project aimed at collecting/synthesizing in public databases, the phenotype, interactome, and genome from 100 specimens each of 1000 species over their distribution range and ecological gradients could attract excitement and major sources of funding and provide significant, novel answers and new questions."

This paper is useful and interesting food for thought for our own Decadal Plan process. The fill paper is at http://www.amjbot.org/content/103/12/2022.full 

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1130785 2017-02-13T04:41:59Z 2017-02-13T04:42:00Z Rob Davis

I'm an identification botanist and taxonomist. I have been with the WA Herbaium for the past 25 years. My initial role with the Herbarium was as a technical assistant, mostly working on WA's bioprospecting project and Regional Forest Assessments, among other survey projects. The past 15 years I have been primarily employed as an identification botanist. In this position, I'm identifying plants from a variety of organisations, either internal identification within the Department of Parks and Wildlife or from environmental consultants, the Department of Agriculture and the general public. I'm also involved in confirming rare and priority taxa for Western Australia. In addition, I'm involved in taxonomy, describing new species from a variety of plant families, but primarily from the genus Ptilotus.

 



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Robert Davis
tag:notobiotica.posthaven.com,2013:Post/1115860 2016-12-15T23:49:13Z 2016-12-15T23:49:13Z Herbaria wilt in the US

From Tanya Schuster, an article from Nature relevant to the Decadal Plan



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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1113781 2016-12-08T06:07:10Z 2016-12-08T07:57:30Z Bushwalk, lunch, sequence genome.

Today, if I wanted, I could go on a bushwalk and sequence a genome.

That might not sound very remarkable as my joints freely bend, I can see, and I don’t mind getting wet, muddy, sweaty and molested by insects, or my skin breached by armed plants and burned by the sun. In fact I sort of enjoy all of those things; well, not individually and in isolation (no, I do not have a dungeon...), but as part of the rich experiential symphony of life in the great outdoors. And being a taxonomist, field work is actually part of my job. I describe life, not in epic poetry, or stunning photography, but in scientific papers that are by some measures, a bit dour. I describe new species – taking the raw, unvarnished thrill that the discovery of an organism unknown to science elicits, and turning it into a scientific manuscript reporting in methodical, formal terms the characteristics of that new organism and giving it a scientific name such that that species becomes available for science and society.

And the life that I describe is found in the bush, and not uncommonly in a country like Australia where about 200 new plant species are described by taxonomists like me every year. THat's an extraordinary figure - 200 new plants a year - and even more startling when you realise it is ten percent of the world’s total. For a taxonomist, Australia really is the lucky country – so many species, and so much bush in which to walk and discover. And with so many new species of plants turning up, discovering a new one is often rather unremarkable.

It is also rather unremarkable that today, I can sequence a genome. I mean unremarkable not in the sense that it is unworthy of awe (because sequencing genomes is awesome), but unremarkable in the sense that everybody, at least in biology and medicine, is doing it. But this socialisation of genomics is very recent. The technology for reading genomes - the sequence of nucleotide bases (A, C, G, T), or ‘letters’ that inscribe the language of life, DNA – has advanced in such a mad headlong rush that by the time the sun set on 2015 it became possible to do in a weekend for less than $2000 something that in the 1990’s took more than a decade and at least half a billion dollars. This extraordinary efficiency gain has outstripped even that most celebrated example of technological advance, the decline in cost of computing power represented by Moore’s Law. This law describes the observation that the number of semiconductors that can be packed onto a silicon chip roughly doubles each year, which roughly translates to a halving of the cost of computing power each 18 months because of the additional savings made through chip manufacturing advances. Because of Moore’s Law my new mobile phone is more powerful in computing terms than my ten year old desktop machine, now unloved and gathering dust under the desk and accidentally assaulted by the toe of my leather winklepickers whenever I yawn and stretch. But the rate of advance in DNA sequencing technology blows Moore’s Law away. It wasn’t always the case. Prior to 2007 the cost of sequencing genomes was falling in line with that of computing power, meaning it could be roughly described by Moore’s Law. Thereafter however, things got really interesting. The cost fell catastrophically because new, more efficient sequencing technologies came online and in the years following drove cost reductions so spectacular that in the time it took computing power to become about 15 times cheaper, sequencing genomes became about 10,000 times cheaper. It’s hard to underestimate the impact this has had on biology and medicine, which are being revolutionised by access to genome data. Even taxonomists like me, working in small labs on small budgets, can now sequence genomes. It is fast becoming a routine, unremarkable, part of the work that we do.

But what is truly remarkable – transformative, disruptive, revolutionary ... whatever – is that it is now technically possible to go for a bushwalk and sequence a genome at the same time and in the same place. I’ll let that sink in.... as a scientist, I am now able to carry all the equipment necessary to sequence a genome into the field with me and sequence the genome of an organism I collect on the spot. Recently, Oxford Nanopore, a biotechnology company based in Oxford, UK, started selling a new DNA sequencing device, the minION. This device is smaller than a mobile phone, plugs into the USB port of a laptop computer, costs about $1000, and can sequence a bacterial genome between lunch and tea. The company is not the only one producing genome sequencing machines, but it is pretty much the only one whose signature device does not require a large, sturdy benchtop to hold it up, a specialist technician to run it, and hundreds of thousands of dollars of cold hard cash to purchase it. This is truly disruptive technology, which is really saying something in the context of a field that has been in constant disruption for nearly ten years. Its a game changer. While some technical details of the device need improvement (its accuracy is still unacceptable for many applications) this early generation product brings us within sight of the day when genome sequencers will be as much part of the field biologist’s toolkit as a GPS unit is now. 

Will this day come? I think so. In fact it will come pretty soon for me. I am hoping to take one with me in March 2017 when I participate in a species discovery expedition on Cape York Peninsula in the remote northeast of Australia. As part of the multiyear BushBlitz species discovery partnership, I will be helping survey Quinkan country, a sandstone landscape renowned for its extensive Aboriginal rock art near the small town of Laura. I’m astounded that I will witness scientists bring samples in from the field that they think may represent species new to science, extract the DNA and offer a small drop to the sequencer who in a few hours will deliver its verdict, confirming or denying their hunches. Imagine the field efficiency gains this will drive: “Jenny, the DNA of that one doesn’t match anything known so very probably a new species. See if you can get more specimens tomorrow.”, or “Boring, just a malnourished and malformed individual of a well known species, don’t bother with any more of that one”. The efficiency gains are important, but rather prosaic. What is deeply inspiring is the utter collapse of the barriers to genome knowledge. A species discovered in the time of the so-called father of taxonomy, Carl von Linne (a.k.a Linnaeus, 1707-1778) would have to wait around 250 years to have its genome revealed. A species discovered today need only wait a few hours...

And what kind of world will this technology usher in for taxonomists and other biologists? What will we do when we are as blase about sequencing whole genomes in the field as we are about cooking our camp dinner? Its hard to fully imagine, but here are a couple of possibilities beyond the obvious “What species is it, what is its population genetic structure and who is it related to phylogenetically?”:

·      Real time species tracking: by discovering DNA discharged downstream by defoliation, defecation or death, field biologists could determine the presence of species of interest upstream and adjust survey plans accordingly.

·      Real time population diversity assessment: by comparing sequences of samples from across the local range of a species one day, researchers may be able to pinpoint the best areas for the following day’s sampling or survey.

This new world is one of great promise and to maximise its opportunities, I want some bright spark to build me a mobile genome lab. I’m thinking a capable 4WD with a raised roof and internally fitted out with a bench, a portable electricity generator and fridge, and the small lab items needed for extracting and purifying DNA to load into the sequencer. And if I pitch this vehicle as the ‘Genome-o-Rover’ then I might just attract the attention and sponsorship dollars of a certain vehicle manufacturer that shall remain nameless. I would volunteer my time to travel the nation, sequencing genomes in situ in the most remote and inhospitable locations, and dropping in to schools and communities along the way to talk about what I am doing. And if I do my job well, I just might find myself a couple of decades from now passing the baton (or sequencer) to some bright eyed graduate who asked me a probing question about plant DNA in the outback 20 years prior.

Who will join me?

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Darren Crayn
tag:notobiotica.posthaven.com,2013:Post/1112937 2016-12-05T03:25:43Z 2016-12-08T07:46:39Z The eFlora of Australia

The Flora of Australia is a standard reference work for Australian vascular plants, providing standard Flora treatments (descriptions, nomenclature, keys, distributions) etc for all covered families, genera and species. The first taxonomic volume of the series was published in 1982 (Volume 8, Lecythidales to Batales). Since then, 25 vascular plant volumes (of a planned 50 volumes) have been published, covering c. 12,000 taxa (including two volumes dealing with Australia’s island territories).

In 2014, a decision was made to discontinue hardcopy publication of the Flora of Australia, and to move instead to a web-based platform. This has obvious advantages: the hardcopy volumes are mostly out-of-print and many are out-of-date, and transitioning to a web platform will allow quicker publication, easier management and updates, and a wider reach to a more diverse audience.

The Atlas of Living Australia (ALA) is creating a new web-based platform for building, managing and maintaining eFloras, including the new eFlora of Australia. Work has commenced to move existing taxonomic treatments from the Flora of Australia to the new platform, including both published and unpublished treatments. Under the editorial management of the Australian Biological Resources Study (ABRS) and supported by an Editorial Committee including representatives from the Council of Heads of Australasian Herbaria (CHAH) and the Australian Systematic Botany Society, the new eFlora platform will allow the eFlora of Australia to be managed and edited using a new, decentralised, community-wide model.

The eFlora of Australia and ALA eFlora platform are not yet ready for public release, but work is progressing well and a release in 2017 is anticipated. Watch this space for more...

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1112927 2016-12-05T00:48:59Z 2017-03-09T14:27:58Z Kevin Thiele

I'm a systematist and taxonomist, a past Director of the Western Australian Herbarium, past Chair of the Council of Heads of Australasian Herbaria, and currently an independent scientist trading under the name Eubio Consulting. After a PhD at Melbourne University, where I worked on an early cladistic analysis of Banksia, I took up a post-doctoral position under Judy West at the Australian National Herbarium, working on a Flora of Australia treatment of Rhamnaceae. My wife and I then eschewed gainful employ and took our small but growing family to a small, off-grid farmlet in a remote and utterly beautiful part of East Gippsland, where we lived and worked for 12 years growing vegetables, raising children, helping out at the local school, and continuing our research work into, amongst other things, the conservation of grassy box woodlands, the taxonomy of Viola, and development of the Lucid suite of software tools. Another major change of lifestyle, occasioned by the children reaching high school age, saw us move to Perth and, for me, the position leading the WA Herbarium for a decade. My current work includes teaching systematics and evolution at the University of Western Australia, the taxonomy of Hibbertia in Western Australia, building an identification key to all Australian flowering plants, and working towards the Decadal Plan for Biosystematics and Taxonomy in Australasia.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1112903 2016-12-04T23:02:43Z 2016-12-08T07:47:52Z The Decadal Plan for Biosystematics and Taxonomy in Australasia

Biosystematics and taxonomy – the disciplines that name, classify and determine the evolutionary relationships of all living organisms – are foundational sciences. Many other disciplines and activities in biology, including ecology, conservation, genetics, biosecurity, and medicine to name just a few, depend on the framework knowledge, nomenclature, and understanding of organisms provided by biosystematics and taxonomy.

Despite this, funding and infrastructure investment in biosystematics and taxonomy are declining. Biosystematics and taxonomy often “fly under the radar” of high-impact science, and their foundational role is often unacknowledged.

The current low base of funding for biosystematics and taxonomy in Australasia means that, in effect, we are drawing on previous investment in this sector (the past two centuries of endeavour and effort to understand and document the flora and fauna of Australasia) but no longer adequately investing in the future (building capacity and knowledge of the many currently known or undiscovered species that have not yet been named, and keeping our knowledge scientifically updated and current). This lack of investment is of particular concern in Australasia, one of very few areas of mega-biodiversity in the world.

Inadequate investment in this sector leads to negative consequences, and often substantial economic costs, for conservation, biosecurity, and sustainable development and growth. Important species will become extinct before they are recognised and their conservation needs and potential ecological and economic roles understood. Emerging biosecurity threats will be recognised too late, compromising early responses and leading to inadequate control measures and increased mitigation costs. These impacts in turn will compromise sustainable development and reduce our ability to minimise the effects of the current global wave of extinctions.

This project seeks to turn this situation around. Led by a core group of leading taxonomists and biosystematists, it centres on developing a Decadal Plan for the scientific discipline of biosystematics and taxonomy in Australasia that will:

  • document current opportunities and risks in the sector;
  • provide a forward-looking vision and roadmap for the discipline, including its impacts on and benefits for biodiversity, society and the economy;
  • provide a detailed investment plan for the next decade; and
  • initiate steps toward implementing the plan through engagement with the sector and its stakeholders.

Decadal Plans have been developed for a number of sectors in Australian science by the Australian Academy of Science - a listing of these can be obtained here

The Decadal Plan for Biosystematics and Taxonomy in Australasia will be a starting point for effecting a real change in the status, visibility and funding of biosystematics and taxonomy in Australasia.

Read the brochure below for more detail


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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1061559 2016-06-09T12:40:43Z 2017-01-20T19:08:25Z Why I reckon there's never been a better time to be an Australian ..... botanist

We've heard from our politicians recently that there's never been a more exciting time to be an Australian. That may or may not be the case. But, here's a story that shows why I reckon there's never been a better time to be an Australian botanist.

Hibbertia huegelii is one of the most common species of Hibbertia in Western Australia. Every botanist, wildflower enthusiast and naturalist knows it. It's common from around Morawa to south of Perth. At least - that's what we thought...

A few weeks ago I realised that I needed to look into H. huegelii when I found that I couldn't figure out exactly how it differs from another, less well-known species in WA, H. pachyrrhiza

I assumed that a quick check through the specimens in the Western Australian Herbarium would sort this out. Pulling out a packet each of H. huegelii and H. pachyrrhiza (while I was at the Herbarium waiting for a student, to head out into the field to collect Banksia specimens for an Honours project), this at first seemed straightforward. The specimens of H. pachyrrhiza I looked at had obtuse leaves with a broad, shallow groove running down the midline, while the first few specimens of H. huegelii had very acute leaves with a distinct, narrow, deep groove along the leaf midline. This worked OK for a while - until I started coming across specimens in the H. huegelii packet that looked a lot like the ones in the H. pachyrrhiza packet. We all know how often something that starts out looking simple quickly becomes less so when you look at too many specimens. I left the Herbarium realising that I'd need to spend more time in the field during the coming spring trying to nut these species out.

An hour later, my student and I with some wonderful colleagues were in Wandoo National Park, at the first site where we were to collect our target Banksia. Getting out of the car, the first plant I saw was H. huegelii. Checking, I noted that it had obtuse leaves with no distinct groove. A metre or so away was another plant of H. huegelii ... that's interesting - this one had acute leaves with a distinct groove. A quick 50-metre walk through the area revealed dozens more plants - and all fell into one of two distinct groups based on these leaf characters. We happened to be in the middle of a mixed population of two distinctly different morphotypes.

That evening (after a successful Banksia field trip) I decided to quickly check to see which of these two morphotypes matched the type of H. huegelii. Global Plants answered that - I searched for the type (scanned from the Naturhistorisches Museum in Vienna) and zoomed into the specimen. It matched, without a doubt, the obtuse-leaved plants. Next step was to check for synonyms of H. huegelii on the Australian Plant Census and in old literature on the Biodiversity Heritage Library. These showed that another name, Candollea striata, had been synonymised with H. huegelii by Bentham in Flora Australiensis. Back to Global Plants, bring up the type of C. striata - this one in Paris - and there were the acute leaves and narrow groove of the other morphotype, as clear as day. It was looking very much like two species rather than one.

The acid test in situations like these is usually to go back into the herbarium. The Western Australian Herbarium holds over 270 specimens of H. huegelii. The next morning I worked through all of these, to see if the difference would hold up. It did - I was able to assign every specimen unambiguously to one or other of the two forms. Over 200 of the specimens matched Candollea striata while nearly 70 specimens matched H. huegelii sensu stricto.

But what of H. pachyrrhiza, one of the species where this story started? This had always seemed more geographically restricted than H. huegelii (as we used to understand it), to the Darling Range just east of Perth between Bindoon and Jarrahdale. Now that I had split H. huegelii into true H. huegelii and C. striata, the next step was to figure out their respective distributions. Scanning the specimen barcodes, I extracted specimen georeferences from the Herbarium database, and popped them into Google Earth to map the distributions. This immediately showed that true H. huegelii and H. pachyrrhiza were almost identically distributed. Having removed C. striata from H. huegelii, they were also morphologically suspiciously similar.

A quick check back at the Biodiversity Heritage Library showed that the original author of H. pachyrrhiza (the German botanist Ernst Steudel) noted that the plant was distinctive in having a thick taproot and numerous short, erect stems with hairy leaves; the specimens at the herbarium bore this out. But - this is exactly what would be expected in fire regrowth. A bit more fieldwork quickly solved the mystery - H. pachyrrhiza is merely post-fire regrowth of H. huegelii

The taxonomic outcome of all this will be a quick paper, to be published in the Western Australian Herbarium's journal Nuytsia, combining C. striata into Hibbertia (as H. striata) and sinking H. pachyrrhiza into a recircumscribed H. huegelii. A small mystery, and an understandable mistake made 150 years ago, solved.

So why is it so great being a botanist? First is the privilege of being able to discover such things. And second is having such great resources to work with - Global Plants, the Biodiversity Heritage Library, Google Earth, our specimen databases (and from those, other resources like the Australian Virtual Herbarium and Atlas of Living Australia). Using these, I was able to have this whole situation pretty much wrapped up and ready to write up in a little over a week, where only a few years ago it would have taken many months.

Only problem is - I didn't need to visit Paris and Vienna to view the type specimens!

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Kevin Thiele